data_2XC6 # _entry.id 2XC6 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.394 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 2XC6 pdb_00002xc6 10.2210/pdb2xc6/pdb PDBE EBI-43667 ? ? WWPDB D_1290043667 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2011-05-04 2 'Structure model' 1 1 2011-10-12 3 'Structure model' 2 0 2022-06-22 4 'Structure model' 2 1 2024-06-19 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' Other 6 3 'Structure model' 'Polymer sequence' 7 4 'Structure model' 'Data collection' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp 2 3 'Structure model' database_2 3 3 'Structure model' entity_poly 4 3 'Structure model' pdbx_database_status 5 3 'Structure model' struct_conn 6 3 'Structure model' struct_site 7 4 'Structure model' chem_comp_atom 8 4 'Structure model' chem_comp_bond # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_chem_comp.mon_nstd_flag' 2 3 'Structure model' '_chem_comp.type' 3 3 'Structure model' '_database_2.pdbx_DOI' 4 3 'Structure model' '_database_2.pdbx_database_accession' 5 3 'Structure model' '_entity_poly.pdbx_seq_one_letter_code_can' 6 3 'Structure model' '_pdbx_database_status.status_code_sf' 7 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 8 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 9 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 10 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2XC6 _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2010-04-16 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Schlegel, M.K.' 1 'Essen, L.-O.' 2 'Meggers, E.' 3 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'On the Structure and Dynamics of Duplex Gna.' J.Org.Chem. 76 7964 ? 2011 JOCEAH US 0022-3263 0035 ? 21838272 10.1021/JO201469B 1 'Duplex Structure of a Minimal Nucleic Acid.' J.Am.Chem.Soc. 130 8158 ? 2008 JACSAT US 0002-7863 0004 ? 18529005 10.1021/JA802788G 2 'Atomic Resolution Duplex Structure of the Simplified Nucleic Acid Gna.' 'Chem.Commun.(Camb.)' 46 1094 ? 2010 ? UK 1359-7345 ? ? 20126724 10.1039/B916851F # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Johnson, A.T.' 1 ? primary 'Schlegel, M.K.' 2 ? primary 'Meggers, E.' 3 ? primary 'Essen, L.O.' 4 ? primary 'Wiest, O.' 5 ? 1 'Schlegel, M.K.' 6 ? 1 'Essen, L.-O.' 7 ? 1 'Meggers, E.' 8 ? 2 'Schlegel, M.K.' 9 ? 2 'Essen, L.-O.' 10 ? 2 'Meggers, E.' 11 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn GNA 2155.194 1 ? ? ? ;SYNTHETIC GLYCOL NUCLEIC ACID 3'-((ZCY)P(ZTH)P(ZCY)P(ZBU)P(ZAD)P(ZGU)P(ZAD)P(ZGU))-2' ; 2 non-polymer syn 'SODIUM ION' 22.990 2 ? ? ? ? 3 water nat water 18.015 21 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(ZCY)(ZTH)(ZCY)(ZBU)(ZAD)(ZGU)(ZAD)(ZGU)' _entity_poly.pdbx_seq_one_letter_code_can CXCUAGAG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SODIUM ION' NA 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ZCY n 1 2 ZTH n 1 3 ZCY n 1 4 ZBU n 1 5 ZAD n 1 6 ZGU n 1 7 ZAD n 1 8 ZGU n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight HOH non-polymer . WATER ? 'H2 O' 18.015 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 ZAD 'RNA linking' n "(S)-1'-(2',3'-DIHYDROXYPROPYL)-ADENINE" ? 'C8 H12 N5 O5 P' 289.185 ZBU 'RNA linking' n "(S)-1'-(2',3'-DIHYDROXYPROPYL)-5-BROMO-URACIL" ? 'C7 H10 Br N2 O7 P' 345.041 ZCY 'RNA linking' n "(S)-1'-(2',3'-DIHYDROXYPROPYL)-CYTOSINE" ? 'C7 H12 N3 O6 P' 265.160 ZGU 'RNA linking' n "(S)-1'-(2',3'-DIHYDROXYPROPYL)-GUANINE" ? 'C8 H12 N5 O6 P' 305.185 ZTH non-polymer . "(S)-1'-(2',3'-DIHYDROXYPROPYL)-THYMINE" ? 'C8 H13 N2 O7 P' 280.172 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 ZCY 1 1 1 ZCY ZCY A . n A 1 2 ZTH 2 2 2 ZTH ZTH A . n A 1 3 ZCY 3 3 3 ZCY ZCY A . n A 1 4 ZBU 4 4 4 ZBU ZBU A . n A 1 5 ZAD 5 5 5 ZAD ZAD A . n A 1 6 ZGU 6 6 6 ZGU ZGU A . n A 1 7 ZAD 7 7 7 ZAD ZAD A . n A 1 8 ZGU 8 8 8 ZGU ZGU A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 NA 1 1001 1001 NA NA A . C 2 NA 1 1002 1002 NA NA A . D 3 HOH 1 2001 2001 HOH HOH A . D 3 HOH 2 2002 2002 HOH HOH A . D 3 HOH 3 2003 2003 HOH HOH A . D 3 HOH 4 2004 2004 HOH HOH A . D 3 HOH 5 2005 2005 HOH HOH A . D 3 HOH 6 2006 2006 HOH HOH A . D 3 HOH 7 2007 2007 HOH HOH A . D 3 HOH 8 2008 2008 HOH HOH A . D 3 HOH 9 2009 2009 HOH HOH A . D 3 HOH 10 2010 2010 HOH HOH A . D 3 HOH 11 2011 2011 HOH HOH A . D 3 HOH 12 2012 2012 HOH HOH A . D 3 HOH 13 2013 2013 HOH HOH A . D 3 HOH 14 2014 2014 HOH HOH A . D 3 HOH 15 2015 2015 HOH HOH A . D 3 HOH 16 2016 2016 HOH HOH A . D 3 HOH 17 2017 2017 HOH HOH A . D 3 HOH 18 2018 2018 HOH HOH A . D 3 HOH 19 2019 2019 HOH HOH A . D 3 HOH 20 2020 2020 HOH HOH A . D 3 HOH 21 2021 2021 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.5.0102 ? 1 XDS 'data reduction' . ? 2 XSCALE 'data scaling' . ? 3 SHELXE phasing . ? 4 # _cell.entry_id 2XC6 _cell.length_a 56.930 _cell.length_b 56.930 _cell.length_c 28.970 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2XC6 _symmetry.space_group_name_H-M 'I 41 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 # _exptl.entry_id 2XC6 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.62 _exptl_crystal.density_percent_sol 56 _exptl_crystal.description NONE # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 5.5 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '10 % MPD, 40 MM SODIUM CACODYLATE, PH 5.5, 20 MM COBALT HEXAMINE, 40 MM LICL, 20 MM MGCL2' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC CCD' _diffrn_detector.pdbx_collection_date 2007-11-24 _diffrn_detector.details MIRRORS # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.91985 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID23-1' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID23-1 _diffrn_source.pdbx_wavelength 0.91985 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 2XC6 _reflns.observed_criterion_sigma_I -3.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 15.88 _reflns.d_resolution_high 1.83 _reflns.number_obs 2242 _reflns.number_all ? _reflns.percent_possible_obs 99.0 _reflns.pdbx_Rmerge_I_obs 0.05 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 32.20 _reflns.B_iso_Wilson_estimate 34.172 _reflns.pdbx_redundancy 17.4 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.83 _reflns_shell.d_res_low 1.93 _reflns_shell.percent_possible_all 98.3 _reflns_shell.Rmerge_I_obs 0.57 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 8.90 _reflns_shell.pdbx_redundancy 17.9 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 2XC6 _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 2068 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 8.00 _refine.ls_d_res_high 1.83 _refine.ls_percent_reflns_obs 99.55 _refine.ls_R_factor_obs 0.23697 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.23447 _refine.ls_R_factor_R_free 0.27060 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 7.0 _refine.ls_number_reflns_R_free 155 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.948 _refine.correlation_coeff_Fo_to_Fc_free 0.921 _refine.B_iso_mean 26.623 _refine.aniso_B[1][1] 1.03 _refine.aniso_B[2][2] 1.03 _refine.aniso_B[3][3] -2.05 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ;HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. GNA DUPLEX OF TYPE N FORMED WITH SYMMETRY-EQUIVALENT MOLECULE, 3'TERMINAL CYTOSINE NUCLEOTIDE AND 5-BROMO ATOM AT U4 ONLY PARTIAL OCCUPANCY. ; _refine.pdbx_starting_model NONE _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.147 _refine.pdbx_overall_ESU_R_Free 0.141 _refine.overall_SU_ML 0.066 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 4.649 _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 137 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 21 _refine_hist.number_atoms_total 160 _refine_hist.d_res_high 1.83 _refine_hist.d_res_low 8.00 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.011 0.021 ? 169 'X-RAY DIFFRACTION' ? r_bond_other_d 0.002 0.020 ? 68 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.715 3.000 ? 213 'X-RAY DIFFRACTION' ? r_angle_other_deg 0.631 3.000 ? 154 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.045 0.200 ? 8 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.007 0.020 ? 84 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.000 0.020 ? 28 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 2.064 3.000 ? 148 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it 2.951 4.500 ? 206 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.832 _refine_ls_shell.d_res_low 1.877 _refine_ls_shell.number_reflns_R_work 138 _refine_ls_shell.R_factor_R_work 0.268 _refine_ls_shell.percent_reflns_obs 96.75 _refine_ls_shell.R_factor_R_free 0.268 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 11 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _database_PDB_matrix.entry_id 2XC6 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 2XC6 _struct.title ;Crystal structure of the GNA 3'-CTC(Br)UAGAG-2' ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2XC6 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA, WATSON-CRICK BASE PAIR, GLYCOL NUCLEIC ACID' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 2 ? D N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2XC6 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession 2XC6 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2XC6 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 8 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2XC6 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 8 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 8 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 15_554 y,x,-z-1 0.0000000000 1.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 -28.9700000000 # _struct_biol.id 1 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale one ? A ZCY 1 O2G ? ? ? 1_555 A ZTH 2 P ? ? A ZCY 1 A ZTH 2 1_555 ? ? ? ? ? ? ? 1.596 ? ? covale2 covale one ? A ZTH 2 O2G ? ? ? 1_555 A ZCY 3 P ? ? A ZTH 2 A ZCY 3 1_555 ? ? ? ? ? ? ? 1.580 ? ? covale3 covale one ? A ZCY 3 O2G ? ? ? 1_555 A ZBU 4 P ? ? A ZCY 3 A ZBU 4 1_555 ? ? ? ? ? ? ? 1.585 ? ? covale4 covale one ? A ZBU 4 O2G ? ? ? 1_555 A ZAD 5 P ? ? A ZBU 4 A ZAD 5 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale5 covale one ? A ZAD 5 O2G ? ? ? 1_555 A ZGU 6 P ? ? A ZAD 5 A ZGU 6 1_555 ? ? ? ? ? ? ? 1.598 ? ? covale6 covale one ? A ZGU 6 O2G ? ? ? 1_555 A ZAD 7 P ? ? A ZGU 6 A ZAD 7 1_555 ? ? ? ? ? ? ? 1.584 ? ? covale7 covale one ? A ZAD 7 O2G ? ? ? 1_555 A ZGU 8 P ? ? A ZAD 7 A ZGU 8 1_555 ? ? ? ? ? ? ? 1.598 ? ? hydrog1 hydrog ? ? A ZCY 1 N3 ? ? ? 1_555 A ZGU 8 N1 ? ? A ZCY 1 A ZGU 8 15_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A ZCY 1 N4 ? ? ? 1_555 A ZGU 8 O6 ? ? A ZCY 1 A ZGU 8 15_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A ZCY 1 O2 ? ? ? 1_555 A ZGU 8 N2 ? ? A ZCY 1 A ZGU 8 15_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A ZTH 2 N3 ? ? ? 1_555 A ZAD 7 N1 ? ? A ZTH 2 A ZAD 7 15_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A ZTH 2 O4 ? ? ? 1_555 A ZAD 7 N6 ? ? A ZTH 2 A ZAD 7 15_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A ZCY 3 N3 ? ? ? 1_555 A ZGU 6 N1 ? ? A ZCY 3 A ZGU 6 15_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A ZCY 3 N4 ? ? ? 1_555 A ZGU 6 O6 ? ? A ZCY 3 A ZGU 6 15_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A ZCY 3 O2 ? ? ? 1_555 A ZGU 6 N2 ? ? A ZCY 3 A ZGU 6 15_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A ZBU 4 N3 ? ? ? 1_555 A ZAD 5 N1 ? ? A ZBU 4 A ZAD 5 15_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A ZBU 4 O4 ? ? ? 1_555 A ZAD 5 N6 ? ? A ZBU 4 A ZAD 5 15_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A ZAD 5 N1 ? ? ? 1_555 A ZBU 4 N3 ? ? A ZAD 5 A ZBU 4 15_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A ZAD 5 N6 ? ? ? 1_555 A ZBU 4 O4 ? ? A ZAD 5 A ZBU 4 15_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A ZGU 6 N1 ? ? ? 1_555 A ZCY 3 N3 ? ? A ZGU 6 A ZCY 3 15_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A ZGU 6 N2 ? ? ? 1_555 A ZCY 3 O2 ? ? A ZGU 6 A ZCY 3 15_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A ZGU 6 O6 ? ? ? 1_555 A ZCY 3 N4 ? ? A ZGU 6 A ZCY 3 15_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A ZAD 7 N1 ? ? ? 1_555 A ZTH 2 N3 ? ? A ZAD 7 A ZTH 2 15_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A ZAD 7 N6 ? ? ? 1_555 A ZTH 2 O4 ? ? A ZAD 7 A ZTH 2 15_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A ZGU 8 N1 ? ? ? 1_555 A ZCY 1 N3 ? ? A ZGU 8 A ZCY 1 15_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A ZGU 8 N2 ? ? ? 1_555 A ZCY 1 O2 ? ? A ZGU 8 A ZCY 1 15_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A ZGU 8 O6 ? ? ? 1_555 A ZCY 1 N4 ? ? A ZGU 8 A ZCY 1 15_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id NA _struct_site.pdbx_auth_seq_id 1002 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 2 _struct_site.details 'BINDING SITE FOR RESIDUE NA A 1002' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 2 ZBU A 4 ? ZBU A 4 . ? 6_554 ? 2 AC1 2 ZBU A 4 ? ZBU A 4 . ? 1_555 ? # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A ZCY 1 A ZCY 1 ? C "(S)-1'-(2',3'-DIHYDROXYPROPYL)-CYTOSINE" 2 A ZTH 2 A ZTH 2 ? T "(S)-1'-(2',3'-DIHYDROXYPROPYL)-THYMINE" 3 A ZCY 3 A ZCY 3 ? C "(S)-1'-(2',3'-DIHYDROXYPROPYL)-CYTOSINE" 4 A ZBU 4 A ZBU 4 ? U ? 5 A ZAD 5 A ZAD 5 ? A "(S)-1'-(2',3'-DIHYDROXYPROPYL)-ADENINE" 6 A ZGU 6 A ZGU 6 ? G "(S)-1'-(2',3'-DIHYDROXYPROPYL)-GUANINE" 7 A ZAD 7 A ZAD 7 ? A "(S)-1'-(2',3'-DIHYDROXYPROPYL)-ADENINE" 8 A ZGU 8 A ZGU 8 ? G "(S)-1'-(2',3'-DIHYDROXYPROPYL)-GUANINE" # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 5.0237 _pdbx_refine_tls.origin_y 6.2082 _pdbx_refine_tls.origin_z -12.2048 _pdbx_refine_tls.T[1][1] 0.0841 _pdbx_refine_tls.T[2][2] 0.1045 _pdbx_refine_tls.T[3][3] 0.0904 _pdbx_refine_tls.T[1][2] -0.0770 _pdbx_refine_tls.T[1][3] 0.0458 _pdbx_refine_tls.T[2][3] -0.0241 _pdbx_refine_tls.L[1][1] 2.0610 _pdbx_refine_tls.L[2][2] 1.8936 _pdbx_refine_tls.L[3][3] 4.7135 _pdbx_refine_tls.L[1][2] 0.4823 _pdbx_refine_tls.L[1][3] 2.3312 _pdbx_refine_tls.L[2][3] -0.6942 _pdbx_refine_tls.S[1][1] 0.0440 _pdbx_refine_tls.S[1][2] -0.3067 _pdbx_refine_tls.S[1][3] 0.0550 _pdbx_refine_tls.S[2][1] -0.1721 _pdbx_refine_tls.S[2][2] 0.0186 _pdbx_refine_tls.S[2][3] -0.0678 _pdbx_refine_tls.S[3][1] -0.7083 _pdbx_refine_tls.S[3][2] 0.6294 _pdbx_refine_tls.S[3][3] -0.0626 # _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.beg_auth_seq_id 1 _pdbx_refine_tls_group.beg_label_asym_id ? _pdbx_refine_tls_group.beg_label_seq_id ? _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 8 _pdbx_refine_tls_group.end_label_asym_id ? _pdbx_refine_tls_group.end_label_seq_id ? _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.selection_details ? # _pdbx_entry_details.entry_id 2XC6 _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;URACIL U4 IS BROMINATED AT C5 FOR MAD ANALYSIS AT BROMINE EDGE ; _pdbx_entry_details.has_ligand_of_interest ? # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal HOH O O N N 1 HOH H1 H N N 2 HOH H2 H N N 3 NA NA NA N N 4 ZAD O2P O N N 5 ZAD P P N N 6 ZAD O1P O N N 7 ZAD O3G O N N 8 ZAD C3G C N N 9 ZAD C2G C N S 10 ZAD O2G O N N 11 ZAD C1G C N N 12 ZAD N9 N Y N 13 ZAD C4 C Y N 14 ZAD N3 N Y N 15 ZAD C2 C Y N 16 ZAD N1 N Y N 17 ZAD C6 C Y N 18 ZAD N6 N N N 19 ZAD C5 C Y N 20 ZAD N7 N Y N 21 ZAD C8 C Y N 22 ZAD OXT O N N 23 ZAD H2P H N N 24 ZAD HOT H N N 25 ZAD H3G1 H N N 26 ZAD H3G2 H N N 27 ZAD H2G H N N 28 ZAD HA H N N 29 ZAD H1G1 H N N 30 ZAD H1G2 H N N 31 ZAD H8 H N N 32 ZAD H2 H N N 33 ZAD H6N1 H N N 34 ZAD H6N2 H N N 35 ZBU O1P O N N 36 ZBU P P N N 37 ZBU O2P O N N 38 ZBU O3G O N N 39 ZBU C3G C N N 40 ZBU C2G C N S 41 ZBU O2G O N N 42 ZBU C1G C N N 43 ZBU N1 N N N 44 ZBU C2 C N N 45 ZBU O2 O N N 46 ZBU N3 N N N 47 ZBU C6 C N N 48 ZBU C5 C N N 49 ZBU BR5 BR N N 50 ZBU C4 C N N 51 ZBU O4 O N N 52 ZBU O3P O N N 53 ZBU H1P H N N 54 ZBU H3P H N N 55 ZBU H3G1 H N N 56 ZBU H3G2 H N N 57 ZBU H2G H N N 58 ZBU HA H N N 59 ZBU H1G1 H N N 60 ZBU H1G2 H N N 61 ZBU H6 H N N 62 ZBU H3 H N N 63 ZCY O2 O N N 64 ZCY C2 C N N 65 ZCY N3 N N N 66 ZCY C4 C N N 67 ZCY N4 N N N 68 ZCY C5 C N N 69 ZCY C6 C N N 70 ZCY N1 N N N 71 ZCY C1G C N N 72 ZCY C2G C N S 73 ZCY O2G O N N 74 ZCY C3G C N N 75 ZCY O3G O N N 76 ZCY P P N N 77 ZCY O2P O N N 78 ZCY O1P O N N 79 ZCY OXT O N N 80 ZCY H4N1 H N N 81 ZCY H4N2 H N N 82 ZCY H5 H N N 83 ZCY H6 H N N 84 ZCY H1G1 H N N 85 ZCY H1G2 H N N 86 ZCY H2G H N N 87 ZCY H3G1 H N N 88 ZCY H3G2 H N N 89 ZCY H2P H N N 90 ZCY H2 H N N 91 ZCY HXT H N N 92 ZGU P P N N 93 ZGU O1P O N N 94 ZGU O2P O N N 95 ZGU O3G O N N 96 ZGU C3G C N N 97 ZGU C2G C N S 98 ZGU O2G O N N 99 ZGU C1G C N N 100 ZGU N9 N Y N 101 ZGU C8 C Y N 102 ZGU N7 N Y N 103 ZGU C4 C Y N 104 ZGU C5 C Y N 105 ZGU N3 N N N 106 ZGU C2 C N N 107 ZGU N2 N N N 108 ZGU N1 N N N 109 ZGU C6 C N N 110 ZGU O6 O N N 111 ZGU OXT O N N 112 ZGU H1P H N N 113 ZGU HOT H N N 114 ZGU H3G1 H N N 115 ZGU H3G2 H N N 116 ZGU H2G H N N 117 ZGU HA H N N 118 ZGU H1G1 H N N 119 ZGU H1G2 H N N 120 ZGU H8 H N N 121 ZGU H2N1 H N N 122 ZGU H2N2 H N N 123 ZGU H1 H N N 124 ZTH O4 O N N 125 ZTH C4 C N N 126 ZTH N3 N N N 127 ZTH C2 C N N 128 ZTH O2 O N N 129 ZTH C5 C N N 130 ZTH C5M C N N 131 ZTH C6 C N N 132 ZTH N1 N N N 133 ZTH C1G C N N 134 ZTH C2G C N S 135 ZTH O2G O N N 136 ZTH C3G C N N 137 ZTH O3G O N N 138 ZTH P P N N 139 ZTH O1P O N N 140 ZTH O2P O N N 141 ZTH H3 H N N 142 ZTH H5M1 H N N 143 ZTH H5M2 H N N 144 ZTH H5M3 H N N 145 ZTH H6 H N N 146 ZTH H1G1 H N N 147 ZTH H1G2 H N N 148 ZTH H2G H N N 149 ZTH H3G1 H N N 150 ZTH H3G2 H N N 151 ZTH H1P H N N 152 ZTH OXT O N N 153 ZTH HXT H N N 154 ZTH H2 H N N 155 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal HOH O H1 sing N N 1 HOH O H2 sing N N 2 ZAD O2P P sing N N 3 ZAD P O1P doub N N 4 ZAD P O3G sing N N 5 ZAD P OXT sing N N 6 ZAD O3G C3G sing N N 7 ZAD C3G C2G sing N N 8 ZAD C2G O2G sing N N 9 ZAD C2G C1G sing N N 10 ZAD C1G N9 sing N N 11 ZAD N9 C4 sing Y N 12 ZAD N9 C8 sing Y N 13 ZAD C4 N3 sing Y N 14 ZAD C4 C5 doub Y N 15 ZAD N3 C2 doub Y N 16 ZAD C2 N1 sing Y N 17 ZAD N1 C6 doub Y N 18 ZAD C6 N6 sing N N 19 ZAD C6 C5 sing Y N 20 ZAD C5 N7 sing Y N 21 ZAD N7 C8 doub Y N 22 ZAD O2P H2P sing N N 23 ZAD OXT HOT sing N N 24 ZAD C3G H3G1 sing N N 25 ZAD C3G H3G2 sing N N 26 ZAD C2G H2G sing N N 27 ZAD O2G HA sing N N 28 ZAD C1G H1G1 sing N N 29 ZAD C1G H1G2 sing N N 30 ZAD C8 H8 sing N N 31 ZAD C2 H2 sing N N 32 ZAD N6 H6N1 sing N N 33 ZAD N6 H6N2 sing N N 34 ZBU O1P P sing N N 35 ZBU P O2P doub N N 36 ZBU P O3G sing N N 37 ZBU P O3P sing N N 38 ZBU O3G C3G sing N N 39 ZBU C3G C2G sing N N 40 ZBU C2G O2G sing N N 41 ZBU C2G C1G sing N N 42 ZBU C1G N1 sing N N 43 ZBU N1 C2 sing N N 44 ZBU N1 C6 sing N N 45 ZBU C2 O2 doub N N 46 ZBU C2 N3 sing N N 47 ZBU N3 C4 sing N N 48 ZBU C6 C5 doub N N 49 ZBU C5 BR5 sing N N 50 ZBU C5 C4 sing N N 51 ZBU C4 O4 doub N N 52 ZBU O1P H1P sing N N 53 ZBU O3P H3P sing N N 54 ZBU C3G H3G1 sing N N 55 ZBU C3G H3G2 sing N N 56 ZBU C2G H2G sing N N 57 ZBU O2G HA sing N N 58 ZBU C1G H1G1 sing N N 59 ZBU C1G H1G2 sing N N 60 ZBU C6 H6 sing N N 61 ZBU N3 H3 sing N N 62 ZCY O2 C2 doub N N 63 ZCY C2 N3 sing N N 64 ZCY C2 N1 sing N N 65 ZCY N3 C4 doub N N 66 ZCY C4 N4 sing N N 67 ZCY C4 C5 sing N N 68 ZCY C5 C6 doub N N 69 ZCY C6 N1 sing N N 70 ZCY N1 C1G sing N N 71 ZCY C1G C2G sing N N 72 ZCY C2G O2G sing N N 73 ZCY C2G C3G sing N N 74 ZCY O2G H2G sing N N 75 ZCY C3G O3G sing N N 76 ZCY O3G P sing N N 77 ZCY P O2P sing N N 78 ZCY P O1P doub N N 79 ZCY N4 H4N1 sing N N 80 ZCY N4 H4N2 sing N N 81 ZCY C5 H5 sing N N 82 ZCY C6 H6 sing N N 83 ZCY C1G H1G1 sing N N 84 ZCY C1G H1G2 sing N N 85 ZCY C2G H2 sing N N 86 ZCY C3G H3G1 sing N N 87 ZCY C3G H3G2 sing N N 88 ZCY O2P H2P sing N N 89 ZCY P OXT sing N N 90 ZCY OXT HXT sing N N 91 ZGU P O1P sing N N 92 ZGU P O2P doub N N 93 ZGU P O3G sing N N 94 ZGU P OXT sing N N 95 ZGU O3G C3G sing N N 96 ZGU C3G C2G sing N N 97 ZGU C2G O2G sing N N 98 ZGU C2G C1G sing N N 99 ZGU C1G N9 sing N N 100 ZGU N9 C8 sing Y N 101 ZGU N9 C4 sing Y N 102 ZGU C8 N7 doub Y N 103 ZGU N7 C5 sing Y N 104 ZGU C4 C5 doub Y N 105 ZGU C4 N3 sing N N 106 ZGU C5 C6 sing N N 107 ZGU N3 C2 doub N N 108 ZGU C2 N2 sing N N 109 ZGU C2 N1 sing N N 110 ZGU N1 C6 sing N N 111 ZGU C6 O6 doub N N 112 ZGU O1P H1P sing N N 113 ZGU OXT HOT sing N N 114 ZGU C3G H3G1 sing N N 115 ZGU C3G H3G2 sing N N 116 ZGU C2G H2G sing N N 117 ZGU O2G HA sing N N 118 ZGU C1G H1G1 sing N N 119 ZGU C1G H1G2 sing N N 120 ZGU C8 H8 sing N N 121 ZGU N2 H2N1 sing N N 122 ZGU N2 H2N2 sing N N 123 ZGU N1 H1 sing N N 124 ZTH O4 C4 doub N N 125 ZTH C4 N3 sing N N 126 ZTH C4 C5 sing N N 127 ZTH N3 C2 sing N N 128 ZTH C2 O2 doub N N 129 ZTH C2 N1 sing N N 130 ZTH C5 C5M sing N N 131 ZTH C5 C6 doub N N 132 ZTH C6 N1 sing N N 133 ZTH N1 C1G sing N N 134 ZTH C1G C2G sing N N 135 ZTH C2G O2G sing N N 136 ZTH C2G C3G sing N N 137 ZTH P OXT sing N N 138 ZTH C3G O3G sing N N 139 ZTH O3G P sing N N 140 ZTH P O1P sing N N 141 ZTH P O2P doub N N 142 ZTH N3 H3 sing N N 143 ZTH C5M H5M1 sing N N 144 ZTH C5M H5M2 sing N N 145 ZTH C5M H5M3 sing N N 146 ZTH C6 H6 sing N N 147 ZTH C1G H1G1 sing N N 148 ZTH C1G H1G2 sing N N 149 ZTH C2G H2G sing N N 150 ZTH C3G H3G1 sing N N 151 ZTH C3G H3G2 sing N N 152 ZTH O1P H1P sing N N 153 ZTH OXT HXT sing N N 154 ZTH O2G H2 sing N N 155 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2XC6 'double helix' 2XC6 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A ZCY 1 1_555 A ZGU 8 15_554 -0.289 -0.007 -0.126 -1.062 -6.768 1.232 1 A_ZCY1:ZGU8_A A 1 ? A 8 ? 19 1 1 A ZTH 2 1_555 A ZAD 7 15_554 0.109 -0.146 -0.013 1.804 2.748 2.183 2 A_ZTH2:ZAD7_A A 2 ? A 7 ? 20 1 1 A ZCY 3 1_555 A ZGU 6 15_554 -0.395 -0.197 0.110 -6.380 -3.722 2.036 3 A_ZCY3:ZGU6_A A 3 ? A 6 ? 19 1 1 A ZBU 4 1_555 A ZAD 5 15_554 0.094 -0.196 0.102 -0.910 -3.976 -2.023 4 A_ZBU4:ZAD5_A A 4 ? A 5 ? 20 1 1 A ZAD 5 1_555 A ZBU 4 15_554 -0.094 -0.196 0.102 0.910 -3.976 -2.023 5 A_ZAD5:ZBU4_A A 5 ? A 4 ? 20 1 1 A ZGU 6 1_555 A ZCY 3 15_554 0.395 -0.197 0.110 6.380 -3.722 2.036 6 A_ZGU6:ZCY3_A A 6 ? A 3 ? 19 1 1 A ZAD 7 1_555 A ZTH 2 15_554 -0.109 -0.146 -0.013 -1.804 2.748 2.183 7 A_ZAD7:ZTH2_A A 7 ? A 2 ? 20 1 1 A ZGU 8 1_555 A ZCY 1 15_554 0.289 -0.007 -0.126 1.062 -6.768 1.232 8 A_ZGU8:ZCY1_A A 8 ? A 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A ZCY 1 1_555 A ZGU 8 15_554 A ZTH 2 1_555 A ZAD 7 15_554 -0.142 -3.317 3.223 0.203 1.673 47.314 -4.263 0.193 3.111 2.083 -0.253 47.343 1 AA_ZCY1ZTH2:ZAD7ZGU8_AA A 1 ? A 8 ? A 2 ? A 7 ? 1 A ZTH 2 1_555 A ZAD 7 15_554 A ZCY 3 1_555 A ZGU 6 15_554 0.103 -4.416 3.491 -0.941 0.872 22.915 -11.420 -0.605 3.316 2.194 2.367 22.950 2 AA_ZTH2ZCY3:ZGU6ZAD7_AA A 2 ? A 7 ? A 3 ? A 6 ? 1 A ZCY 3 1_555 A ZGU 6 15_554 A ZBU 4 1_555 A ZAD 5 15_554 0.042 -3.157 3.072 -0.195 3.999 46.119 -4.322 -0.068 2.804 5.093 0.248 46.283 3 AA_ZCY3ZBU4:ZAD5ZGU6_AA A 3 ? A 6 ? A 4 ? A 5 ? 1 A ZBU 4 1_555 A ZAD 5 15_554 A ZAD 5 1_555 A ZBU 4 15_554 0.000 -4.124 3.216 0.000 6.601 26.451 -10.126 0.000 2.142 14.148 0.000 27.248 4 AA_ZBU4ZAD5:ZBU4ZAD5_AA A 4 ? A 5 ? A 5 ? A 4 ? 1 A ZAD 5 1_555 A ZBU 4 15_554 A ZGU 6 1_555 A ZCY 3 15_554 -0.042 -3.157 3.072 0.195 3.999 46.119 -4.322 0.068 2.804 5.093 -0.248 46.283 5 AA_ZAD5ZGU6:ZCY3ZBU4_AA A 5 ? A 4 ? A 6 ? A 3 ? 1 A ZGU 6 1_555 A ZCY 3 15_554 A ZAD 7 1_555 A ZTH 2 15_554 -0.103 -4.416 3.491 0.941 0.872 22.915 -11.420 0.605 3.316 2.194 -2.367 22.950 6 AA_ZGU6ZAD7:ZTH2ZCY3_AA A 6 ? A 3 ? A 7 ? A 2 ? 1 A ZAD 7 1_555 A ZTH 2 15_554 A ZGU 8 1_555 A ZCY 1 15_554 0.142 -3.317 3.223 -0.203 1.673 47.314 -4.263 -0.193 3.111 2.083 0.253 47.343 7 AA_ZAD7ZGU8:ZCY1ZTH2_AA A 7 ? A 2 ? A 8 ? A 1 ? # _atom_sites.entry_id 2XC6 _atom_sites.fract_transf_matrix[1][1] 0.017565 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.017565 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.034518 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol BR C N NA O P # loop_